PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• RNA binding proteins (RBPs) and messenger RNAs (mRNAs) are crucial for post-transcriptional gene regulation.
• Current methods for mapping RNA-RBP interactions are often protein-centered, limiting the exploration of the entire RBPome.
• There is a need for gene-centered techniques to identify RBPs that interact with a specific mRNA.

Purpose of the Study:

• To introduce a novel gene-centered assay, Protein-RNA Interaction Mapping Assay (PRIMA), for mapping RNA-RBP interactions.
• To demonstrate PRIMA's capability in identifying RBPs that bind to a given RNA molecule.
• To provide a complementary tool for a more comprehensive exploration of the RNA-RBP interactome.

Main Methods:

• PRIMA is a translation-based assay performed in the yeast cytoplasm.
• The assay uses an RNA 'bait' to test interactions with multiple RBP 'preys' simultaneously.
• PRIMA was tested with small RNA elements and full-length Caenorhabditis elegans 3' UTRs.

Main Results:

• PRIMA successfully recapitulated known RNA-RBP interactions.
• The assay identified novel RNA-RBP interactions, with some validated in vivo.
• PRIMA demonstrated versatility with different RNA types and lengths.

Conclusions:

• PRIMA offers a powerful gene-centered approach to study RNA-RBP interactions.
• This assay expands the scale and depth of RNA-RBP interactome exploration.
• PRIMA serves as a valuable complementary tool to existing protein-centered methods.